From 96418f3d32daf7f2154f2fd471e8d82c4c378137 Mon Sep 17 00:00:00 2001 From: d33bs Date: Thu, 14 Aug 2025 17:00:27 -0600 Subject: [PATCH 1/5] add more explicit note about zarr dependency --- pyproject.toml | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/pyproject.toml b/pyproject.toml index c5c96cab..9bb16091 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -33,7 +33,8 @@ anndata = [ { version = "<0.12.2", python = "<3.11" }, { version = ">=0.12.2", python = ">=3.11" }, ] -# zarr is required by anndata <0.12.2 +# Explicit zarr dependency for +# anndata <0.12.2 and Python <3.11 zarr = [ { version = "<3.1.1", python = "<3.11" }, { version = ">=3.1.1", python = ">=3.11" }, From 4bfc956954e9cf01e14536adb120248febe6e17d Mon Sep 17 00:00:00 2001 From: d33bs Date: Thu, 14 Aug 2025 17:00:44 -0600 Subject: [PATCH 2/5] add distinguishing notes about related projects --- readme.md | 12 +++++++++++- 1 file changed, 11 insertions(+), 1 deletion(-) diff --git a/readme.md b/readme.md index e7b4c914..8ba995e6 100644 --- a/readme.md +++ b/readme.md @@ -15,7 +15,7 @@ _Diagram showing data flow relative to this project._ CytoTable enables single-cell morphology data analysis by cleaning and transforming CellProfiler (`.csv` or `.sqlite`), cytominer-database (`.sqlite`), and DeepProfiler (`.npz`), and other sources such as IN Carta data output data at scale. CytoTable creates parquet files for both independent analysis and for input into [Pycytominer](https://github.com/cytomining/pycytominer). -The Parquet files will have a unified and documented data model, including referenceable schema where appropriate (for validation within Pycytominer or other projects). +The output files (such as [Parquet](https://parquet.apache.org/) and [anndata](https://github.com/scverse/anndata) file formats) have a documented data model, including referenceable schema where appropriate (for validation within Pycytominer or other image-based profiling projects). The name for the project is inspired from: @@ -42,6 +42,16 @@ We test CytoTable using `ubuntu-latest` and `macos-latest` [GitHub Actions runne Please see [contributing.md](docs/source/contributing.md) for more details on contributions, development, and testing. +## Relationship to other projects + +CytoTable focuses on image-based profiling data harmonization and serialization to file formats. +It creates data which can be directly integrated with: +- [Pycytominer](https://github.com/cytomining/pycytominer) for image-based profiling analysis. +- [coSMicQC](https://github.com/cytomining/coSMicQC) for single-cell morphology quality control. +- [CytoDataFrame](https://github.com/cytomining/CytoDataFrame) to visualize image-based profiling feature data alongside images within Jupyter environments. + +Please let us know how you use CytoTable (we'd love to add your project to this list)! + ## References - [pycytominer](https://github.com/cytomining/pycytominer) From 5dc27a5146fb3b397464b9899c0c7123a3848a71 Mon Sep 17 00:00:00 2001 From: d33bs Date: Thu, 14 Aug 2025 17:03:04 -0600 Subject: [PATCH 3/5] linting --- pyproject.toml | 2 +- readme.md | 1 + 2 files changed, 2 insertions(+), 1 deletion(-) diff --git a/pyproject.toml b/pyproject.toml index 9bb16091..063df66f 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -33,7 +33,7 @@ anndata = [ { version = "<0.12.2", python = "<3.11" }, { version = ">=0.12.2", python = ">=3.11" }, ] -# Explicit zarr dependency for +# Explicit zarr dependency for # anndata <0.12.2 and Python <3.11 zarr = [ { version = "<3.1.1", python = "<3.11" }, diff --git a/readme.md b/readme.md index 8ba995e6..2f63013a 100644 --- a/readme.md +++ b/readme.md @@ -46,6 +46,7 @@ Please see [contributing.md](docs/source/contributing.md) for more details on co CytoTable focuses on image-based profiling data harmonization and serialization to file formats. It creates data which can be directly integrated with: + - [Pycytominer](https://github.com/cytomining/pycytominer) for image-based profiling analysis. - [coSMicQC](https://github.com/cytomining/coSMicQC) for single-cell morphology quality control. - [CytoDataFrame](https://github.com/cytomining/CytoDataFrame) to visualize image-based profiling feature data alongside images within Jupyter environments. From 61f85d66ae154be6b415e0124243ca79ebc9a628 Mon Sep 17 00:00:00 2001 From: Dave Bunten Date: Mon, 18 Aug 2025 16:58:00 -0600 Subject: [PATCH 4/5] Apply suggestions from code review Co-authored-by: Gregory Way --- readme.md | 12 ++++++------ 1 file changed, 6 insertions(+), 6 deletions(-) diff --git a/readme.md b/readme.md index 2f63013a..1fd52811 100644 --- a/readme.md +++ b/readme.md @@ -44,14 +44,14 @@ Please see [contributing.md](docs/source/contributing.md) for more details on co ## Relationship to other projects -CytoTable focuses on image-based profiling data harmonization and serialization to file formats. -It creates data which can be directly integrated with: +CytoTable focuses on image-based profiling data harmonization and serialization. +At scale, CytoTable transforms data into file formats which can be directly integrated with: -- [Pycytominer](https://github.com/cytomining/pycytominer) for image-based profiling analysis. -- [coSMicQC](https://github.com/cytomining/coSMicQC) for single-cell morphology quality control. -- [CytoDataFrame](https://github.com/cytomining/CytoDataFrame) to visualize image-based profiling feature data alongside images within Jupyter environments. +- [Pycytominer](https://github.com/cytomining/pycytominer) for the bioinformatics pipeline for image-based profiling. +- [coSMicQC](https://github.com/cytomining/coSMicQC) for quality control. +- [CytoDataFrame](https://github.com/cytomining/CytoDataFrame) for interactive visualization of profiles with single cell images. -Please let us know how you use CytoTable (we'd love to add your project to this list)! +**Please let us know how you use CytoTable (we'd love to add your project to this list)**! ## References From 2295496d5c925a87516f3ab3baea1cc80237fa4a Mon Sep 17 00:00:00 2001 From: d33bs Date: Mon, 18 Aug 2025 17:00:14 -0600 Subject: [PATCH 5/5] move add to list mention to top of list Co-Authored-By: Gregory Way --- readme.md | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/readme.md b/readme.md index 1fd52811..dbf966e1 100644 --- a/readme.md +++ b/readme.md @@ -47,12 +47,12 @@ Please see [contributing.md](docs/source/contributing.md) for more details on co CytoTable focuses on image-based profiling data harmonization and serialization. At scale, CytoTable transforms data into file formats which can be directly integrated with: +**Please let us know how you use CytoTable (we'd love to add your project to this list)**! + - [Pycytominer](https://github.com/cytomining/pycytominer) for the bioinformatics pipeline for image-based profiling. - [coSMicQC](https://github.com/cytomining/coSMicQC) for quality control. - [CytoDataFrame](https://github.com/cytomining/CytoDataFrame) for interactive visualization of profiles with single cell images. -**Please let us know how you use CytoTable (we'd love to add your project to this list)**! - ## References - [pycytominer](https://github.com/cytomining/pycytominer)